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monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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mondolib migration #393

Open joeflack4 opened 6 months ago

joeflack4 commented 6 months ago

Overview

Migrate all Python code to mondolib.

Implementation

Package management

In requirements.txt and requirements-unlocked.txt, there would be an entry for mondolib.

Python

In Python files, if any do happen to continue to exist in mondo-ingest, would do:

from mondolib import my_func

Makefile

In mondo-ingest.Makefile goals:

my_output.tsv:
    mondolib MY_COMMAND VARIOUS_PARAMS --output-path $@

Making sure the package is installed: a. Add a pip-mondolib prereq to all the goals that need it, b. Do pip-mondolib at the start of build-mondo-ingest c. Do a pip install -r requirements.txt at start of build-mondo-ingest

twhetzel commented 6 months ago

Just a note, if and what to migrate into mondolib is still To Be Decided, but good to have this placeholder ticket.